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Background: Malaria remains a major public health threat in Burkina Faso. In most sub-Saharan African countries, malaria control relies mainly on long-lasting insecticide-treated nets (LLINs) and indoor residual spray (IRS). In Burkina Faso, long-term selection pressure exerted on malaria vectors by insecticide used in agriculture, has been exacerbated by countrywide LLINs distribution campaigns conducted every three years since 2010. The current study investigated insecticide resistance and the mechanisms involved in the malaria vector populations of the Anopheles gambiae complex in urban localities of Ouagadougou, Burkina Faso. Methods: Anopheles gambiae s. l. larvae were collected from three localities of Ouagadougou from July to September 2018, and reared in the laboratory to adults. The susceptibility profile to pyrethroid, carbamate, and organophosphate insecticides was assessed using World Health Organization (WHO) tube assays. PCR was used for mosquito species identification and to detect insecticide target-site mutations involved in insecticide resistance. Results: More than 95% of the collected An. gambiae s. l. were identified as An. arabiensis. WHO susceptibility assays revealed that, in all localities, An. arabiensis displayed high resistance to permethrin and deltamethrin (mortalities both kdr mutations 1014F (0.81) and 1014S (0.18) were recorded, although carbamate and organophosphate-associated Ace-1 119S mutation was not found. Conclusion: High pyrethroid resistance, underpinned, at least in part by high-frequency knockdown resistance mutations, in the urban malaria vector population suggests the potentially poor performance of pyrethroid-only LLINs in the cities where they are distributed. This result supported the switch to next generation LLINs, which are not solely reliant on pyrethroids to kill host-seeking mosquitoes in the cities of Burkina Faso.